SYNOPSIS

DESCRIPTION

This interface defines the basic set of methods an object should have to manipulate assembly data.

FEEDBACK

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Support

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bioperl-l@bioperl.org

rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible.

Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web:

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AUTHOR - Robson Francisco de Souza

Email: rfsouza@citri.iq.usp.br

APPENDIX

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

Accessing general assembly data

get_nof_contigs

Title : get_nof_contigs
Usage : $assembly->get_nof_contigs()
Function: Get the number of contigs included in the assembly
Returns : integer
Args : none

get_nof_singlets

Title : get_nof_singlets
Usage : $assembly->get_nof_singlets()
Function: Get the number of singlets included in the assembly
Returns : integer
Args : none

get_contig_ids

Title : get_contig_ids
Usage : $assembly->get_contig_ids()
Function: Access list of contig IDs from assembly
Returns : an array if there are any contigs in the assembly.
undef otherwise
Args : an array of contig IDs

get_singlet_ids

Title : get_singlet_ids
Usage : $assembly->get_singlet_ids()
Function: Access list of singlet IDs from assembly
Returns : an array if there are any singlets in the assembly.
undef otherwise
Args : an array of singlet IDs

get_contig_by_id

Title : get_contig_by_id
Usage : $assembly->get_contig_by_id($id)
Function: Get a reference for a contig from the assembly
Returns : a Bio::Assembly::Contig object or undef
Args : [string] contig unique identifier (ID)

get_singlet_by_id

Title : get_singlet_by_id
Usage : $assembly->get_singlet_by_id()
Function: Get a reference for a singlet from the assembly
Returns : Bio::Assembly::Singlet object or undef
Args : [string] a singlet ID

Modifier methods

Implementation of these methods is optional in the sense that read-only implementations may not have these. If an object implements one of them, it should however implement all.

Contig and singlet selection methos

select_contigs

Title : select_contig
Usage : $assembly->select_contig
Function: Selects an array of contigs from the assembly
Returns : an array of Bio::Assembly::Contig objects
Args : an array of contig ids
See function get_contig_ids() above

select_singlets

Title : select_singlets
Usage : $assembly->select_singlets(@list)
Function: Selects an array of singlets from the assembly
Returns : an array of Bio::Assembly::Singlet objects
Args : an array of singlet ids
See function get_singlet_ids() above

all_contigs

Title : all_contigs
Usage : my @contigs = $assembly->all_contigs
Function: Returns a list of all contigs in this assembly.
Contigs are both clusters and alignments of one
or more reads, with an associated consensus
sequence.
Returns : array of Bio::Assembly::Contig
Args : none

all_singlets

Title : all_singlets
Usage : my @singlets = $assembly->all_singlets
Function: Returns a list of all singlets in this assembly.
Singlets are isolated reads, without non-vector
matches to any other read in the assembly.
Returns : array of Bio::Assembly::Singlet objects
Args : none